Fix docs (#54) #269
Annotations
10 warnings and 1 notice
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L46
failed to run `@setup` block in src/math.md
```@setup ex_tri
using DelaunayTriangulation, CairoMakie
θ = LinRange(0, 2π, 50)
θ = collect(θ)
θ[end] = θ[begin]
g = θ -> cos(θ) - sin(3θ) + sin(5θ)
ε = 1 / 10
x = @. (1 + g(θ) * ε) * cos(θ)
y = @. (1 + g(θ) * ε) * sin(θ)
h = θ -> cos(3θ) - sin(θ)
ε = 1 / 5
x2 = @. 0.5(1 + h(θ) * ε) * cos(θ)
y2 = @. 0.5(1 + h(θ) * ε) * sin(θ)
reverse!(x2)
reverse!(y2)
boundary_nodes, points = convert_boundary_points_to_indices([[x], [x2]], [[y], [y2]])
tri = triangulate(points; boundary_nodes, delete_ghosts=false)
refine!(tri)
fig, ax, sc = triplot(tri,
show_convex_hull=false,
show_constrained_edges=false,
show_all_points=true,
point_color=:black)
hidedecorations!(ax)
```
exception =
LoadError: Invalid attributes point_color and show_all_points for plot type MakieCore.Plot{Makie.triplot, Tuple{DelaunayTriangulation.Triangulation{Vector{Tuple{Float64, Float64}}, Set{Tuple{Int64, Int64, Int64}}, Vector{Vector{Vector{Int64}}}, DelaunayTriangulation.ZeroWeight{Float64}, Int64, Tuple{Int64, Int64}, Set{Tuple{Int64, Int64}}, Tuple{}, Dict{Tuple{Int64, Int64}, Tuple{Tuple{Int64, Int64}, Int64}}, Dict{Int64, Tuple{Int64, Int64}}, Dict{Int64, UnitRange{Int64}}, Dict{Int64, DelaunayTriangulation.RepresentativeCoordinates{Int64, Float64}}, DelaunayTriangulation.TriangulationCache{DelaunayTriangulation.Triangulation{Vector{Tuple{Float64, Float64}}, Set{Tuple{Int64, Int64, Int64}}, Vector{Int64}, DelaunayTriangulation.ZeroWeight{Float64}, Int64, Tuple{Int64, Int64}, Set{Tuple{Int64, Int64}}, Tuple{}, Dict{Tuple{Int64, Int64}, Tuple{Vector{Int64}, Int64}}, Dict{Int64, Vector{Int64}}, Dict{Int64, UnitRange{Int64}}, Dict{Int64, DelaunayTriangulation.RepresentativeCoordinates{Int64, Float64}}, DelaunayTriangulation.TriangulationCache{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, Nothing}, Vector{Int64}, Set{Tuple{Int64, Int64}}, Vector{Int64}, Set{Tuple{Int64, Int64, Int64}}, NTuple{4, SubArray{Float64, 1, Vector{Float64}, Tuple{UnitRange{Int64}}, true}}, Tuple{SubArray{Float64, 1, Vector{Float64}, Tuple{UnitRange{Int64}}, true}, SubArray{Float64, 1, Vector{Float64}, Tuple{UnitRange{Int64}}, true}}, NTuple{27, SubArray{Float64, 1, Vector{Float64}, Tuple{UnitRange{Int64}}, true}}}, Nothing}}}.
The available plot attributes for MakieCore.Plot{Makie.triplot, Tuple{DelaunayTriangulation.Triangulation{Vector{Tuple{Float64, Float64}}, Set{Tuple{Int64, Int64, Int64}}, Vector{Vector{Vector{Int64}}}, DelaunayTriangulation.ZeroWeight{Float64}, Int64, Tuple{Int64, Int64}, Set{Tuple{Int64, Int64}}, Tuple{}, Dict{Tuple{Int64, Int64}, Tuple{Tuple{Int64, Int64}, Int64}}, Dict{Int64, Tuple{Int64, Int64}}, Dict{Int64, UnitRange{Int64}}, Dict{Int64, DelaunayTriangulation.RepresentativeCoordinates{Int64, Float64}}, DelaunayTriangulation.TriangulationCache{DelaunayTriangulation.Triangulation{Vector{Tuple{Float64, Float64}}, Set{Tuple{Int64, Int64, Int64}}, Vector{Int64}, DelaunayTriangulation.ZeroWeight{Float64}, Int64, Tuple{Int64, Int64}, Set{Tuple{Int64, Int64}}, Tuple{}, Dict{Tuple{Int64, Int64}, Tuple{Vector{Int64}, Int64}}, Dict{Int64, Vector{Int64}}, Dict{Int64, UnitRange{Int64}}, Dict{Int64, DelaunayTriangulation.RepresentativeCoordinates{Int64, Float64}}, DelaunayTriangulation.TriangulationCache{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, Nothing}, Vector{Int64}, Set{Tuple{Int64, Int64}}, Vector{Int64}, Set{Tuple{Int64, Int64, Int64}}, NTuple{4, SubArray{Float64, 1, Vector{Float64}, Tuple{UnitRange{Int64}}, true}}, Tuple{SubArray{Float64, 1, Vector{Float64}, Tuple{UnitRange{Int64}}, true}, SubArray{Float64, 1, Vector{Float64}, Tuple{UnitRange{Int64}}, true}}, NTuple{27, SubArray{Float64, 1, Vector{Float64}, Tuple{UnitRange{Int64}}, true}}}, Nothing}}} are:
bounding_box ghost_edge_linestyle recompute_centers
constrained_edge_color ghost_edge_linewidth show_constrained_edges
constrained_edge_linestyle joinstyle show_convex_hull
constrained_edge_linewidth linecap
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L46
failed to run `@example` block in src/math.md:50-52
```@example ex_tri
fig #hide
```
exception =
UndefVarError: `fig` not defined
Stacktrace:
[1] top-level scope
@ :0
[2] eval
@ ./boot.jl:385 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L46
failed to run `@setup` block in src/math.md
```@setup ex_tri
centroids = NTuple{2,Float64}[]
linesegments = NTuple{2,Float64}[]
for T in each_solid_triangle(tri)
i, j, k = triangle_vertices(T)
p, q, r = get_point(tri, i, j, k)
cent = DelaunayTriangulation.triangle_centroid(p, q, r)
push!(centroids, cent)
u, v, w = DelaunayTriangulation.triangle_edge_midpoints(p, q, r)
push!(linesegments, cent, u, cent, v, cent, w)
end
linesegments!(ax, linesegments, color=:blue)
scatter!(ax, centroids, color=:red, markersize=8)
```
exception =
LoadError: UndefVarError: `ax` not defined
Stacktrace:
[1] top-level scope
@ string:11
[2] eval
@ ./boot.jl:385 [inlined]
[3] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
@ Base ./loading.jl:2076
[4] include_string (repeats 2 times)
@ ./loading.jl:2086 [inlined]
[5] #67
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:907 [inlined]
[6] cd(f::Documenter.var"#67#68"{Module, MarkdownAST.CodeBlock}, dir::String)
@ Base.Filesystem ./file.jl:112
[7] runner(::Type{Documenter.Expanders.SetupBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:906
in expression starting at string:11
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L46
failed to run `@example` block in src/math.md:50-52
```@example ex_tri
fig #hide
```
exception =
UndefVarError: `fig` not defined
Stacktrace:
[1] top-level scope
@ :0
[2] eval
@ ./boot.jl:385 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L46
failed to run `@setup` block in src/math.md
```@setup cv_notation
using DelaunayTriangulation, CairoMakie, LinearAlgebra
a, b, c, d, e, f = (0.0, 0.0),
(2.0, 3.0),
(4.0, -1.0),
(1.0, -4.0),
(-4.0, -2.0),
(-4.0, 2.0)
points = [a, b, c, d, e, f]
tri = triangulate(points)
centroids = NTuple{2,Float64}[]
linesegments = NTuple{2,Float64}[]
other_linesegments = NTuple{2,Float64}[]
non_cv_midpoints = collect.([
(f .+ b) ./ 2,
(b .+ c) ./ 2,
(c .+ d) ./ 2,
(d .+ e) ./ 2,
(e .+ f) ./ 2
])
for T in each_solid_triangle(tri)
i, j, k = triangle_vertices(T)
p, q, r = get_point(tri, i, j, k)
cent = DelaunayTriangulation.triangle_centroid(p, q, r)
push!(centroids, cent)
u, v, w = DelaunayTriangulation.triangle_edge_midpoints(p, q, r)
any(≈(collect(u)), non_cv_midpoints) ? push!(other_linesegments, cent, u) : push!(linesegments, cent, u)
any(≈(collect(v)), non_cv_midpoints) ? push!(other_linesegments, cent, v) : push!(linesegments, cent, v)
any(≈(collect(w)), non_cv_midpoints) ? push!(other_linesegments, cent, w) : push!(linesegments, cent, w)
end
control_volume_verts = vcat(linesegments, centroids)
cv_idx = collect(eachindex(control_volume_verts))
DelaunayTriangulation.sort_convex_polygon!(cv_idx, control_volume_verts)
fig, ax, sc = poly(control_volume_verts[cv_idx],
color=:lightgreen,
axis=(width=400, height=400))
triplot!(tri,
show_convex_hull=false,
show_constrained_edges=false,
show_all_points=true,
point_color=:black,
markersize=11)
scatter!(ax, [a, b, c], color=:cyan, markersize=11, strokecolor=:black, strokewidth=1)
linesegments!(ax, linesegments, color=:blue, linewidth=3)
linesegments!(ax, other_linesegments, color=(:grey, 0.5))
cidx = findfirst(≈(collect((f .+ a .+ b) ./ 3)), collect.(centroids))
lidx = findfirst(≈(collect((f .+ a) ./ 2)), collect.(linesegments))
u, v = centroids[cidx], linesegments[lidx]
rot90_uv = [0 -1; 1 0] * collect(u .- v)
rot90_uv = 0.8rot90_uv ./ norm(rot90_uv)
m = (u .+ v) ./ 2
p = scatter!(ax, [m], color=:blue, markersize=11, strokecolor=:black, strokewidth=1)
arrows!(ax, [m[1]], [m[2]], [rot90_uv[1]], [rot90_uv[2]], color=:black)
lines!(ax, [u, v], color=:magenta, linewidth=3)
translate!(p, 0, 0, 1)
scatter!(ax, centroids, color=:red, markersize=11, strokecolor=:black, strokewidth=1)
text!(ax, -0.8, -1.7, text=L"\Omega_i", fontsize=24)
text!(ax, -3.2, -1.0, text=L"\partial\Omega_i", fontsize=24)
text!(ax, -2.0, 1.1, text=L"\sigma", fontsize=24)
text!(ax, -2.4, 1.6, text=L"\hat{\mathbf{n}}_{\sigma}", fontsize=24)
text!(ax, -1.4, 0.8, text=L"\mathbf{x}_{\sigma}", fontsize=24)
text!(ax, 0.2, 0.0, text=L"\mathbf{x}_{i}", fontsize=24)
text!(ax, 0.2, -0.5, text=L"v_{k1}", fontsize=24)
text!(ax, 3.1, -1.3, text=L"v_{k2}", fontsize=24)
text!(ax, 2.1, 2.9, text=L"v_{k3}", fontsize=24)
text!(ax, 1.7, 1.5, text=L"T_k", fontsize=24)
hidedecorations!(ax)
resize_to_layout!(fig)
```
exception =
LoadError: Invalid attributes point_color and show_all_points for plot type MakieCore.Plot{Makie.triplot, Tuple{DelaunayTriangulation.Triangulation{Vector{Tuple{Float64, Float64}}, Set{Tuple{Int64, Int64, Int64}}, Vector{Int64}, DelaunayTriangulation.ZeroWeight{Float64}, Int64, Tuple{Int64, Int64}, Set{Tuple{Int64, Int64}}, Tuple{}, Dict{Tuple{Int64, Int64}, Tuple{Vector{Int64}, Int64}}, Dict{Int64, Vector{Int64}}, Dict{Int64, UnitRange{Int64}}, Dict{Int64, DelaunayTriangulation.RepresentativeCoordinates{Int64, Float64}}, DelaunayTriangulation.TriangulationCache{DelaunayTriangulation.Triangulation{Vector{Tuple{Float64, Float64}}, Set{Tuple{Int64, Int64, Int64}}, Vector{Int64}, DelaunayTriangulation.ZeroWeight{Float64}, Int64, Tuple{Int64, Int64}, Set{Tuple{Int64, Int64}}, Tuple{}, Dict{Tuple{Int64, Int64}, Tuple{Vector{Int64}, Int64}}, Dict{Int64, Vector{Int64}}, Dict{Int64, UnitRange{Int64}}, Dict{Int64, DelaunayTriangulation.RepresentativeCoordinates{Int64, Float64}}, DelaunayTriangulation.TriangulationCache{Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing}, Nothing}, Vector{Int64}, Set{Tuple{Int64, Int64}}, V
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L46
failed to run `@example` block in src/wyos/diffusion_equations.md:399-421
```@example diffusion_equations
BCs_prob = BoundaryConditions(mesh, (x, y, t, u, p) -> -4, Neumann)
fvm_prob = FVMProblem(mesh, BCs_prob;
diffusion_function=let D = diffusion_function
(x, y, t, u, p) -> D(x, y, p)
end,
initial_condition,
final_time)
fvm_sol = solve(fvm_prob, TRBDF2(linsolve=KLUFactorization()); saveat=100.0)
fvm_sol |> tc #hide
for j in eachindex(fvm_sol)
ax = Axis(fig[2, j], width=600, height=600,
xlabel="x", ylabel="y",
title="t = $(fvm_sol.t[j])",
titlealign=:left)
u = j == 1 ? initial_condition : fvm_sol.u[j]
tricontourf!(ax, tri, u, levels=0:0.1:1, colormap=:turbo, extendlow=:auto, extendhigh=:auto)
tightlimits!(ax)
end
resize_to_layout!(fig)
fig
```
exception =
UndefVarError: `KLUFactorization` not defined
Stacktrace:
[1] top-level scope
@ diffusion_equations.md:407
[2] eval
@ ./boot.jl:385 [inlined]
[3] #60
@ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined]
[4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String)
@ Base.Filesystem ./file.jl:112
[5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})()
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753
[6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})()
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170
[7] with_logstate(f::Function, logstate::Any)
@ Base.CoreLogging ./logging.jl:515
[8] with_logger
@ ./logging.jl:627 [inlined]
[9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any})
@ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167
[10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document)
@ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/C1XEF/src/html/HTMLWriter.jl#L807
For 56 @example blocks, the 'text/html' representation of the resulting
object is above the threshold (example_size_threshold: 8192 bytes).
- 56 blocks had 'image/png' fallback image representation available, using that.
On pages: math.md, tutorials/diffusion_equation_in_a_wedge_with_mixed_boundary_conditions.md, tutorials/diffusion_equation_on_a_square_plate.md, tutorials/diffusion_equation_on_an_annulus.md, tutorials/equilibrium_temperature_distribution_with_mixed_boundary_conditions_and_using_ensembleproblems.md, tutorials/helmholtz_equation_with_inhomogeneous_boundary_conditions.md, tutorials/laplaces_equation_with_internal_dirichlet_conditions.md, tutorials/mean_exit_time.md, tutorials/overview.md, tutorials/piecewise_linear_and_natural_neighbour_interpolation_for_an_advection_diffusion_equation.md, tutorials/porous_fisher_equation_and_travelling_waves.md, tutorials/porous_medium_equation.md, tutorials/reaction_diffusion_brusselator_system_of_pdes.md, tutorials/reaction_diffusion_equation_with_a_time_dependent_dirichlet_boundary_condition_on_a_disk.md, tutorials/solving_mazes_with_laplaces_equation.md, wyos/diffusion_equations.md, wyos/laplaces_equation.md, wyos/linear_reaction_diffusion_equations.md, wyos/mean_exit_time.md, wyos/poissons_equation.md
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/C1XEF/src/deploydocs.jl#L533
removing `stable` and linking `stable` to `v1.1.4`.
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/C1XEF/src/deploydocs.jl#L533
removing `v1.1` and linking `v1.1` to `v1.1.4`.
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Run julia-actions/julia-docdeploy@v1:
../../../.julia/packages/Documenter/C1XEF/src/deploydocs.jl#L533
removing `v1.0` and linking `v1.0` to `v1.0.0`.
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Run julia-actions/julia-buildpkg@v1
Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`
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